I have started to look into KNIME for node develpment in the Mass Spectrometry (Chemistry) area.
Recently I have run into problems using external jars. The approach outlined in the Developers FAQ works well for simple jars and my node executes fine. However, if I try to run more complex jars that have several dependencies (all of them included in the jar), I run into errors such as:
Execute failed: org.openscience.cdk.tools.manipulator.AtomContainerManipulator.getTotalExactMass(Lorg/openscience/cdk/interfaces/IAtomContainer;)D
I have tested the jar in other projects with identical parameters. No problems.
Is there anything in particular that need to be taken care off when it comes to jar imports? Or do you happen to have any other suggestions why CDK fails inside the jar?
Looking forward to your replies,
Do you the the KNIME CDK extension installed, too? Then you will very likely run into class loading problems if you use your own CDK jars. KNIME's version unfortunately is quite outdated, but there is work in progress with a more recent version.
Thanks for the quick and helpful reply.
"Unfortunately", I have the KNIME CDK extension installed. I need the CDKMolecule data type and functionality for my nodes.
Is there any way to resolve the problem? I.e., use the CDK extension but force my external jar to use the libs provided within the plugin itself rather than the CDK ones?
You plugin is already using you JAR files, but the new classes are incompatible to the ones used by the KNIME plugin. This is where the error message comes from. Unfortunately there is no solution to this problem until a new version of the CDK plugin is ready.
Okay, that's rather bad news.
Is anyone already working on a new version of the CDK plugin? If so, when can one expect a release?